Align L-lactate dehydrogenase iron-sulfur cluster-binding protein LldF (characterized, see rationale)
to candidate 8499630 DvMF_0396 iron-sulfur cluster binding protein (RefSeq)
Query= uniprot:Q8EGS5 (464 letters) >FitnessBrowser__Miya:8499630 Length = 475 Score = 282 bits (721), Expect = 2e-80 Identities = 163/393 (41%), Positives = 226/393 (57%), Gaps = 16/393 (4%) Query: 10 MGSQVHAYKADI---FCRDETRVDWHSKALWLLREKRDRAAGSLPEWEQLRQLGSEIKLH 66 MGSQ + A++ + R ++ S AL L +KR E E++R K Sbjct: 1 MGSQHLDFTANVTEALADRQLRANFKS-ALTGLMKKRVAVLPDAAERERMRDDAEAAKRK 59 Query: 67 TLTNLAQYLETFEQNCLANGIKVHWAKDGAEHNRIVHEILASHKVKKLVKSKSMLTEECH 126 L L + LE E+ C NGI VHWA+ AE N I+ +I+ SH +LVK KSM++EE H Sbjct: 60 ALAKLPELLERLERKCTENGIIVHWAETTAEANEIILDIMRSHDATRLVKGKSMVSEEMH 119 Query: 127 LNPYLEQRGIEVIDTDLGERIIQLAKMPPSHIVVPAIHMKKEEVGDLFHDKLGTKAGESD 186 LN +LE GIE ++TDLGE IIQL PPSHI+VPA+H +++VG +F D L Sbjct: 120 LNHFLETHGIEALETDLGEFIIQLNHEPPSHIIVPAVHKNRQQVGRIFADNLQGIPYTDV 179 Query: 187 PLYLTRAARAHLREQFLSADAAMTGVNMAIADKGAVVVCTNEGNADMGANLPKLQLHSMG 246 L AR LRE+F + ++GVN A+A+ G +V+ NEGN M +P + + MG Sbjct: 180 VEELNAIARKTLREKFRTGHVGLSGVNFAVAETGTLVLVENEGNGRMCTTVPPVHVAVMG 239 Query: 247 IDKVVPDIDSAAVLLRTLARNATGQPVTTYSAFYRGPQVDG------EMHVIIVDNGRTE 300 ++KVV + LLR L +ATGQ VTTY P+ DG E+H++I+DNGR+ Sbjct: 240 LEKVVESLSDLPPLLRLLTASATGQLVTTYVNCITSPRKDGERDGPKEIHLVILDNGRSR 299 Query: 301 MMKDKILAESLKCIRCGGCLNTCPVYRRSGGYSYNYTIPGPIGIAVGATHD---NTNSIA 357 M+ D L +L+CIRCG CLN CPVY R GG++Y PGPIG + D + +A Sbjct: 300 MLADAQLRRTLQCIRCGTCLNHCPVYIRIGGHAYGSVYPGPIGKILTPQIDGLADKGVLA 359 Query: 358 WACTLCGSCTYVCPTKVPLDKIIHHHRRLKAEA 390 A +LC +C VCP ++P+ II RR++ EA Sbjct: 360 TASSLCNACEEVCPVRIPIPGII---RRMRTEA 389 Lambda K H 0.320 0.134 0.413 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 512 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 464 Length of database: 475 Length adjustment: 33 Effective length of query: 431 Effective length of database: 442 Effective search space: 190502 Effective search space used: 190502 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory